cwltool.command_line_tool ========================= .. py:module:: cwltool.command_line_tool .. autoapi-nested-parse:: Implementation of CommandLineTool. Attributes ---------- .. autoapisummary:: cwltool.command_line_tool.OutputPortsType Exceptions ---------- .. autoapisummary:: cwltool.command_line_tool.ParameterOutputWorkflowException Classes ------- .. autoapisummary:: cwltool.command_line_tool.PathCheckingMode cwltool.command_line_tool.ExpressionJob cwltool.command_line_tool.ExpressionTool cwltool.command_line_tool.AbstractOperation cwltool.command_line_tool.CallbackJob cwltool.command_line_tool.CommandLineTool Functions --------- .. autoapisummary:: cwltool.command_line_tool.remove_path cwltool.command_line_tool.revmap_file cwltool.command_line_tool.check_adjust cwltool.command_line_tool.check_valid_locations Module Contents --------------- .. py:class:: PathCheckingMode(*args, **kwds) Bases: :py:obj:`enum.Enum` .. autoapi-inheritance-diagram:: cwltool.command_line_tool.PathCheckingMode :parts: 1 What characters are allowed in path names. We have the strict (default) mode and the relaxed mode. .. py:attribute:: STRICT Accepts names that contain one or more of the following: .. list-table:: * - ``\w`` - unicode word characters this includes most characters that can be part of a word in any language, as well as numbers and the underscore * - ``.`` - a literal period * - ``+`` - a literal plus sign * - ``,`` - a literal comma * - ``-`` - a literal minus sign * - ``:`` - a literal colon * - ``@`` - a literal at-symbol * - ``]`` - a literal end-square-bracket * - ``^`` - a literal caret symbol * - ``\u2600-\u26FF`` - matches a single character in the range between ☀ (index 9728) and ⛿ (index 9983) * - ``\U0001f600-\U0001f64f`` - matches a single character in the range between 😀 (index 128512) and 🙏 (index 128591) Note: the following characters are intentionally not included: 1. reserved words in POSIX: ``!``, :code:`{`, ``}`` 2. POSIX metacharacters listed in the CWL standard as okay to reject: ``|``, ``&``, ``;``, ``<``, ``>``, ``(``, ``)``, ``$``, `````, ``"``, ``'``, :kbd:``, :kbd:``, :kbd:``. (In accordance with https://www.commonwl.org/v1.0/CommandLineTool.html#File under "path" ) 3. POSIX path separator: ``\`` (also listed at https://www.commonwl.org/v1.0/CommandLineTool.html#File under "path") 4. Additional POSIX metacharacters: ``*``, ``?``, ``[``, ``#``, ``˜``, ``=``, ``%``. TODO: switch to https://pypi.org/project/regex/ and use ``\p{Extended_Pictographic}`` instead of the manual emoji ranges .. py:attribute:: RELAXED Accept anything. .. py:class:: ExpressionJob(builder, script, output_callback, requirements, hints, outdir = None, tmpdir = None) Job for :py:class:`ExpressionTool`. .. py:attribute:: builder .. py:attribute:: requirements .. py:attribute:: hints .. py:attribute:: output_callback .. py:attribute:: outdir :value: None .. py:attribute:: tmpdir :value: None .. py:attribute:: script .. py:attribute:: prov_obj :type: Optional[cwltool.cwlprov.provenance_profile.ProvenanceProfile] :value: None .. py:method:: run(runtimeContext, tmpdir_lock = None) .. py:class:: ExpressionTool(toolpath_object, loadingContext) Bases: :py:obj:`cwltool.process.Process` .. autoapi-inheritance-diagram:: cwltool.command_line_tool.ExpressionTool :parts: 1 Abstract CWL Process. .. py:method:: job(job_order, output_callbacks, runtimeContext) .. py:class:: AbstractOperation(toolpath_object, loadingContext) Bases: :py:obj:`cwltool.process.Process` .. autoapi-inheritance-diagram:: cwltool.command_line_tool.AbstractOperation :parts: 1 Abstract CWL Process. .. py:method:: job(job_order, output_callbacks, runtimeContext) .. py:function:: remove_path(f) Remove any 'path' property, if present. .. py:function:: revmap_file(builder, outdir, f) Remap a file from internal path to external path. For Docker, this maps from the path inside tho container to the path outside the container. Recognizes files in the pathmapper or remaps internal output directories to the external directory. .. py:class:: CallbackJob(job, output_callback, cachebuilder, jobcache) Callback Job class, used by :py:func:`CommandLineTool.job`. .. py:attribute:: job .. py:attribute:: output_callback .. py:attribute:: cachebuilder .. py:attribute:: outdir .. py:attribute:: prov_obj :type: cwltool.cwlprov.provenance_profile.ProvenanceProfile | None :value: None .. py:method:: run(runtimeContext, tmpdir_lock = None) .. py:function:: check_adjust(accept_re, builder, file_o) Map files to assigned path inside a container. We need to also explicitly walk over input, as implicit reassignment doesn't reach everything in builder.bindings .. py:function:: check_valid_locations(fs_access, ob) .. py:data:: OutputPortsType .. py:exception:: ParameterOutputWorkflowException(msg, port) Bases: :py:obj:`cwltool.errors.WorkflowException` .. autoapi-inheritance-diagram:: cwltool.command_line_tool.ParameterOutputWorkflowException :parts: 1 Common base class for all non-exit exceptions. .. py:attribute:: msg .. py:attribute:: port .. py:method:: __str__() Return str(self). .. py:class:: CommandLineTool(toolpath_object, loadingContext) Bases: :py:obj:`cwltool.process.Process` .. autoapi-inheritance-diagram:: cwltool.command_line_tool.CommandLineTool :parts: 1 Abstract CWL Process. .. py:attribute:: prov_obj .. py:attribute:: path_check_mode :type: PathCheckingMode .. py:method:: make_job_runner(runtimeContext) Return the correct CommandLineJob class given the container settings. .. py:method:: make_path_mapper(reffiles, stagedir, runtimeContext, separateDirs) :staticmethod: .. py:method:: updatePathmap(outdir, pathmap, fn) Update a PathMapper with a CWL File or Directory object. .. py:method:: job(job_order, output_callbacks, runtimeContext) .. py:method:: collect_output_ports(ports, builder, outdir, rcode, compute_checksum = True, jobname = '', readers = None) .. py:method:: collect_output(schema, builder, outdir, fs_access, compute_checksum = True)